Low order equivalent system models were identified from flight test data for the Tu-144LL supersonic transport aircraft. Flight test maneuvers were executed by Russian and American test Pilots flying the aircraft from Zhukovsky airfield outside Moscow, Russia. Flight tests included longitudinal and lateral / directional maneuvers at supersonic cruise flight conditions. Piloted frequency sweeps and multi-step maneuvers were used to generate data for closed loop low order equivalent system modeling. Model parameters were estimated using a flexible. high accuracy Fourier transform and an equation error / output error (EE/OE) formulation in the frequency domain. Results were compared to parameter estimates obtained using spectral estimation and subsequent least squares fit to frequency response data in Bode plots. Modeling results from the two methods agreed well for both a frequency sweep and multiple concatenated multi-step maneuvers. For a single multi-step maneuvers the EE/OE method gave a better model fit with improved prediction capability. A summary of closed loop low order equivalent system identification results for the Tu-144LL, including estimated parameters, standard errors, and flying qualities level predictions, were computed and tabulated.